Researchers at the National Human Genome Research Institute (NHGRI) at the National Institutes of Health (NIH), in collaboration with the University of Tampere in Finland and the University of Basel in Switzerland, have developed a new research tool which they call the “tissue chip.” The tissue chip has enabled researchers to distinguish among subgroups of cancer patients and eventually predict which subgroups will respond to specific therapies. Such detailed new information can then be used to identify critical molecules for development of cancer therapies.
The tissue chip is a thin section of a biological microarray that permits massive parallel processing of biological samples, making it possible for researchers to simultaneously compare an array of biological samples for molecular markers, DNA, RNA, and proteins in tissues from hundreds or thousands of samples. As many as one thousand individual samples can be studied in a single biological microarray, thus making it practical to simultaneously test thousands of biological samples when researchers would traditionally analyze one sample at a time. The power of this technology is expected to reduce analysis time and reduce the costs of reagents used in the analysis thus accelerating research while reducing costs.
Early methods of generating biological microarrays generally include removing tissue slices or cores from paraffin blocks and re-embedding these. For example, Battifora, U.S. Pat. No. 4,820,504 teaches forming multiple tissue samples into rods, bundling the rods into a casing, embedding the encased rods in paraffin and sectioning them. Although the method arrays multiple tissue samples, the method requires a high degree of manual dexterity, and often makes it difficult to find and identify particular samples of interest.
Battifora, U.S. Pat. No. 5,002,377 describes cutting tissue samples into strips, positioning the strips into parallel grooves in a mold, and embedding the strips in paraffin. The strips are stacked to form an embedded block comprising of multiple tissue samples. This method has improved the ability to identify the location of samples but is still very time consuming and is performed manually.
In order to construct biological microarrays in an efficient and precise manner, several apparatus have been recently described to transfer a multitude of biological materials into an array form within an embedding medium. All of the art describes using two separately mounted punches: the donor punch for coring and transferring the donor sample and the recipient punch for preparing a receptacle to receive the donor sample. The outside diameter of the recipient punch is nearly equivalent to the inside diameter of the donor punch.
Much of the disclosed art describes apparatus to manipulate the two punches, donor and recipient, relative to each other and with respect to a donor and recipient block. The donor punch is precisely positioned over the recipient block when transferring the sample to the predetermined receptacle with minimal, if not any, repositioning.
Leighton, U.S. Pat. No. 6,103,518 describes an apparatus that positions two punches, the recipient punch and the donor punch, on a displaceable mechanism such that each punch will be precisely positioned against stops or detents. The stops or detents require initial and periodic adjustment in order to maintain the concentricity of the two punches while in their operational positions and after punch replacement.
Leighton, U.S. Pat. No. 6,383,801 describes an apparatus that drives the two separate punches separately in the Z-axis, and periodically recalibrates the punch concentricity in order to properly align to donor punch to a receptacle made previously by the recipient punch. The device requires an offset measurement sensor, and efficiency is reduced by the subsequent measurement and correction times.
Chasse et al., U.S. patent application Publication 20030017446 also describes a similar situation where a calibration process is required between the donor punch and the recipient coring device in order to properly align to donor punch to a receptacle made previously by the recipient punch. Again, an offset measurement sensor and subsequent measurement and correction times are required.
Leighton, U.S. Pat. No. 6,468,783 and Leighton, U.S. patent application Publication 20040197897 each describe an apparatus with a mechanism for automatically changing two or more punches in and out of a holder on the Z-axis. The mechanism will align the two respective punches concentrically. But the time, however small, to locate a punch, grip, and move to the desired location for operation reduces the efficiency of the device. The mechanism and the grippers required to change the punches is mechanically complex.
Kononen et al., U.S. Pat. No. 6,699,710, the entirety of which is incorporated herein by reference, describes a first embodiment apparatus for creating tissue microarrays. A donor punch is positioned relative to a donor block to core a sample from a region of interest as identified by positioning a reference slide over the donor block. The punch is lowered to cut the core and raised to removed the core of interest. The donor block is replaced with the recipient block containing an array of receptacles and the punch apparatus is repositioned to be above a predetermined receptacle. The core is deposited into the receptacle using a stylus.
Kononen et al. teaches that the recipient block consists of an array of receptacles produced in a similar manner to the coring of the donor block prior to the donor transferring process. The coring of array receptacles, however, produces poor positional results as the density of the array increases and the diameter of the core decreases. The embedding media is not perfectly solid and does not cut cleanly; a first cored and unfilled receptacle is more likely to be displaced or distorted by an adjacent receptacle coring than if the first receptacle was filled prior to the second receptacle coring.
Kononen et al. also discloses a second embodiment apparatus for creating tissue microarrays. The second apparatus is an automated device that continues the use of two separate donor and recipient punches. The punches are mounted such that they can be positioned below a single stylus during operation so that the same stylus is aligned and inserted into the punches. The mismatch in punch diameters with the same stylus distorts the donor core during deposition into the receptacle. Distortion increases as donor core size decreases with higher density tissue microarrays.
Thus there is a need for an improved microarrayer for constructing biological arrays in an embedding medium. The improved microarrayer should be less complex in construction and more efficient in operation. The improved microarrayer should enable a receptacle in a recipient block be filled prior to forming an adjacent receptacle, and deformation of the donor core should be minimized during deposition into the receptacle.